src/jalview/gui/AnnotationColourChooser.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
   3  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  */
  18 package jalview.gui;
  19
  20 import java.util.*;
  21
  22 import java.awt.*;
  23 import java.awt.event.*;
  24 import javax.swing.*;
  25 import javax.swing.event.*;
  26
  27 import jalview.bin.Cache;
  28 import jalview.datamodel.*;
  29 import jalview.schemes.*;
  30 import java.awt.Dimension;
  31
  32 public class AnnotationColourChooser extends JPanel
  33 {
  34   JInternalFrame frame;
  35
  36   AlignViewport av;
  37
  38   AlignmentPanel ap;
  39
  40   ColourSchemeI oldcs;
  41
  42   Hashtable oldgroupColours;
  43
  44   jalview.datamodel.AlignmentAnnotation currentAnnotation;
  45
  46   boolean adjusting = false;
  47
  48   public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
  49   {
  50     oldcs = av.getGlobalColourScheme();
  51     if (av.alignment.getGroups() != null)
  52     {
  53       oldgroupColours = new Hashtable();
  54       Vector allGroups = ap.av.alignment.getGroups();
  55       SequenceGroup sg;
  56       for (int g = 0; g < allGroups.size(); g++)
  57       {
  58         sg = (SequenceGroup) allGroups.get(g);
  59         if (sg.cs != null)
  60         {
  61           oldgroupColours.put(sg, sg.cs);
  62         }
  63       }
  64     }
  65     this.av = av;
  66     this.ap = ap;
  67     frame = new JInternalFrame();
  68     frame.setContentPane(this);
  69     frame.setLayer(JLayeredPane.PALETTE_LAYER);
  70     Desktop.addInternalFrame(frame, "Colour by Annotation", 480, 145);
  71
  72     slider.addChangeListener(new ChangeListener()
  73     {
  74       public void stateChanged(ChangeEvent evt)
  75       {
  76         if (!adjusting)
  77         {
  78           thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
  79           valueChanged();
  80         }
  81       }
  82     });
  83     slider.addMouseListener(new MouseAdapter()
  84     {
  85       public void mouseReleased(MouseEvent evt)
  86       {
  87         ap.paintAlignment(true);
  88       }
  89     });
  90
  91     if (av.alignment.getAlignmentAnnotation() == null)
  92     {
  93       return;
  94     }
  95
  96     // Always get default shading from preferences.
  97     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
  98     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
  99
 100     if (oldcs instanceof AnnotationColourGradient)
 101     {
 102       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 103       currentColours.setSelected(acg.predefinedColours);
 104       if (acg.predefinedColours)
 105       {
 106
 107       } else {
 108         minColour.setBackground(acg.getMinColour());
 109         maxColour.setBackground(acg.getMaxColour());
 110       }
 111     }
 112
 113     adjusting = true;
 114     Vector list = new Vector();
 115     int index = 1;
 116     for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
 117     {
 118       String label = av.alignment.getAlignmentAnnotation()[i].label;
 119       if (!list.contains(label))
 120         list.addElement(label);
 121       else
 122         list.addElement(label + "_" + (index++));
 123     }
 124
 125     annotations = new JComboBox(list);
 126
 127     threshold.addItem("No Threshold");
 128     threshold.addItem("Above Threshold");
 129     threshold.addItem("Below Threshold");
 130
 131     if (oldcs instanceof AnnotationColourGradient)
 132     {
 133       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 134       annotations.setSelectedItem(acg.getAnnotation());
 135       switch (acg.getAboveThreshold()) {
 136       case AnnotationColourGradient.NO_THRESHOLD:
 137           threshold.setSelectedItem("No Threshold");
 138         break;
 139       case AnnotationColourGradient.ABOVE_THRESHOLD:
 140           threshold.setSelectedItem("Above Threshold");
 141         break;
 142       case AnnotationColourGradient.BELOW_THRESHOLD:
 143         threshold.setSelectedItem("Below Threshold");
 144         break;
 145         default:
 146           throw new Error("Implementation error: don't know about threshold setting for current AnnotationColourGradient.");
 147       }
 148       thresholdIsMin.setSelected(acg.thresholdIsMinMax);
 149       thresholdValue.setText(""+acg.getAnnotationThreshold());
 150     }
 151
 152     try
 153     {
 154       jbInit();
 155     } catch (Exception ex)
 156     {
 157     }
 158
 159     adjusting = false;
 160
 161     changeColour();
 162     validate();
 163
 164   }
 165
 166   public AnnotationColourChooser()
 167   {
 168     try
 169     {
 170       jbInit();
 171     } catch (Exception ex)
 172     {
 173       ex.printStackTrace();
 174     }
 175   }
 176
 177   private void jbInit() throws Exception
 178   {
 179     minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 180     minColour.setBorder(BorderFactory.createEtchedBorder());
 181     minColour.setPreferredSize(new Dimension(40, 20));
 182     minColour.setToolTipText("Minimum Colour");
 183     minColour.addMouseListener(new MouseAdapter()
 184     {
 185       public void mousePressed(MouseEvent e)
 186       {
 187         if (minColour.isEnabled())
 188         {
 189           minColour_actionPerformed();
 190         }
 191       }
 192     });
 193     maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 194     maxColour.setBorder(BorderFactory.createEtchedBorder());
 195     maxColour.setPreferredSize(new Dimension(40, 20));
 196     maxColour.setToolTipText("Maximum Colour");
 197     maxColour.addMouseListener(new MouseAdapter()
 198     {
 199       public void mousePressed(MouseEvent e)
 200       {
 201         if (maxColour.isEnabled())
 202         {
 203           maxColour_actionPerformed();
 204         }
 205       }
 206     });
 207     ok.setOpaque(false);
 208     ok.setText("OK");
 209     ok.addActionListener(new ActionListener()
 210     {
 211       public void actionPerformed(ActionEvent e)
 212       {
 213         ok_actionPerformed(e);
 214       }
 215     });
 216     cancel.setOpaque(false);
 217     cancel.setText("Cancel");
 218     cancel.addActionListener(new ActionListener()
 219     {
 220       public void actionPerformed(ActionEvent e)
 221       {
 222         cancel_actionPerformed(e);
 223       }
 224     });
 225     this.setLayout(borderLayout1);
 226     jPanel2.setLayout(flowLayout1);
 227     annotations.addActionListener(new ActionListener()
 228     {
 229       public void actionPerformed(ActionEvent e)
 230       {
 231         annotations_actionPerformed(e);
 232       }
 233     });
 234     jPanel1.setBackground(Color.white);
 235     jPanel2.setBackground(Color.white);
 236     threshold.addActionListener(new ActionListener()
 237     {
 238       public void actionPerformed(ActionEvent e)
 239       {
 240         threshold_actionPerformed(e);
 241       }
 242     });
 243     jPanel3.setLayout(flowLayout2);
 244     thresholdValue.addActionListener(new ActionListener()
 245     {
 246       public void actionPerformed(ActionEvent e)
 247       {
 248         thresholdValue_actionPerformed(e);
 249       }
 250     });
 251     slider.setPaintLabels(false);
 252     slider.setPaintTicks(true);
 253     slider.setBackground(Color.white);
 254     slider.setEnabled(false);
 255     slider.setOpaque(false);
 256     slider.setPreferredSize(new Dimension(100, 32));
 257     thresholdValue.setEnabled(false);
 258     thresholdValue.setColumns(7);
 259     jPanel3.setBackground(Color.white);
 260     currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
 261     currentColours.setOpaque(false);
 262     currentColours.setText("Use Original Colours");
 263     currentColours.addActionListener(new ActionListener()
 264     {
 265       public void actionPerformed(ActionEvent e)
 266       {
 267         currentColours_actionPerformed(e);
 268       }
 269     });
 270     thresholdIsMin.setBackground(Color.white);
 271     thresholdIsMin.setText("Threshold is Min/Max");
 272     thresholdIsMin.addActionListener(new ActionListener()
 273     {
 274       public void actionPerformed(ActionEvent actionEvent)
 275       {
 276         thresholdIsMin_actionPerformed(actionEvent);
 277       }
 278     });
 279     jPanel1.add(ok);
 280     jPanel1.add(cancel);
 281     jPanel2.add(annotations);
 282     jPanel2.add(currentColours);
 283     jPanel2.add(minColour);
 284     jPanel2.add(maxColour);
 285     this.add(jPanel3, java.awt.BorderLayout.CENTER);
 286     jPanel3.add(threshold);
 287     jPanel3.add(slider);
 288     jPanel3.add(thresholdValue);
 289     jPanel3.add(thresholdIsMin);
 290     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 291     this.add(jPanel2, java.awt.BorderLayout.NORTH);
 292   }
 293
 294   JComboBox annotations;
 295
 296   JPanel minColour = new JPanel();
 297
 298   JPanel maxColour = new JPanel();
 299
 300   JButton ok = new JButton();
 301
 302   JButton cancel = new JButton();
 303
 304   JPanel jPanel1 = new JPanel();
 305
 306   JPanel jPanel2 = new JPanel();
 307
 308   BorderLayout borderLayout1 = new BorderLayout();
 309
 310   JComboBox threshold = new JComboBox();
 311
 312   FlowLayout flowLayout1 = new FlowLayout();
 313
 314   JPanel jPanel3 = new JPanel();
 315
 316   FlowLayout flowLayout2 = new FlowLayout();
 317
 318   JSlider slider = new JSlider();
 319
 320   JTextField thresholdValue = new JTextField(20);
 321
 322   JCheckBox currentColours = new JCheckBox();
 323
 324   JCheckBox thresholdIsMin = new JCheckBox();
 325
 326   public void minColour_actionPerformed()
 327   {
 328     Color col = JColorChooser.showDialog(this,
 329             "Select Colour for Minimum Value", minColour.getBackground());
 330     if (col != null)
 331     {
 332       minColour.setBackground(col);
 333     }
 334     minColour.repaint();
 335     changeColour();
 336   }
 337
 338   public void maxColour_actionPerformed()
 339   {
 340     Color col = JColorChooser.showDialog(this,
 341             "Select Colour for Maximum Value", maxColour.getBackground());
 342     if (col != null)
 343     {
 344       maxColour.setBackground(col);
 345     }
 346     maxColour.repaint();
 347     changeColour();
 348   }
 349
 350   void changeColour()
 351   {
 352     // Check if combobox is still adjusting
 353     if (adjusting)
 354     {
 355       return;
 356     }
 357
 358     currentAnnotation = av.alignment.getAlignmentAnnotation()[annotations
 359             .getSelectedIndex()];
 360
 361     int aboveThreshold = -1;
 362     if (threshold.getSelectedItem().equals("Above Threshold"))
 363     {
 364       aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
 365     }
 366     else if (threshold.getSelectedItem().equals("Below Threshold"))
 367     {
 368       aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
 369     }
 370
 371     slider.setEnabled(true);
 372     thresholdValue.setEnabled(true);
 373
 374     if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
 375     {
 376       slider.setEnabled(false);
 377       thresholdValue.setEnabled(false);
 378       thresholdValue.setText("");
 379     }
 380     else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
 381             && currentAnnotation.threshold == null)
 382     {
 383       currentAnnotation
 384               .setThreshold(new jalview.datamodel.GraphLine(
 385                       (currentAnnotation.graphMax - currentAnnotation.graphMin) / 2f,
 386                       "Threshold", Color.black));
 387     }
 388
 389     if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
 390     {
 391       adjusting = true;
 392       float range = currentAnnotation.graphMax * 1000
 393               - currentAnnotation.graphMin * 1000;
 394
 395       slider.setMinimum((int) (currentAnnotation.graphMin * 1000));
 396       slider.setMaximum((int) (currentAnnotation.graphMax * 1000));
 397       slider.setValue((int) (currentAnnotation.threshold.value * 1000));
 398       thresholdValue.setText(currentAnnotation.threshold.value + "");
 399       slider.setMajorTickSpacing((int) (range / 10f));
 400       slider.setEnabled(true);
 401       thresholdValue.setEnabled(true);
 402       adjusting = false;
 403     }
 404
 405     AnnotationColourGradient acg = null;
 406     if (currentColours.isSelected())
 407     {
 408       acg = new AnnotationColourGradient(currentAnnotation,
 409               av.getGlobalColourScheme(), aboveThreshold);
 410     }
 411     else
 412     {
 413       acg = new AnnotationColourGradient(currentAnnotation,
 414               minColour.getBackground(), maxColour.getBackground(),
 415               aboveThreshold);
 416     }
 417
 418     if (currentAnnotation.graphMin == 0f
 419             && currentAnnotation.graphMax == 0f)
 420     {
 421       acg.predefinedColours = true;
 422     }
 423
 424     acg.thresholdIsMinMax = thresholdIsMin.isSelected();
 425
 426     av.setGlobalColourScheme(acg);
 427
 428     if (av.alignment.getGroups() != null)
 429     {
 430       Vector allGroups = ap.av.alignment.getGroups();
 431       SequenceGroup sg;
 432       for (int g = 0; g < allGroups.size(); g++)
 433       {
 434         sg = (SequenceGroup) allGroups.get(g);
 435
 436         if (sg.cs == null)
 437         {
 438           continue;
 439         }
 440
 441         if (currentColours.isSelected())
 442         {
 443           sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
 444                   aboveThreshold);
 445         }
 446         else
 447         {
 448           sg.cs = new AnnotationColourGradient(currentAnnotation,
 449                   minColour.getBackground(), maxColour.getBackground(),
 450                   aboveThreshold);
 451         }
 452
 453       }
 454     }
 455     // ensure all associated views (overviews, structures, etc) are notified of updated colours.
 456     ap.paintAlignment(true);
 457   }
 458
 459   public void ok_actionPerformed(ActionEvent e)
 460   {
 461     changeColour();
 462     try
 463     {
 464       frame.setClosed(true);
 465     } catch (Exception ex)
 466     {
 467     }
 468   }
 469
 470   public void cancel_actionPerformed(ActionEvent e)
 471   {
 472     reset();
 473     try
 474     {
 475       frame.setClosed(true);
 476     } catch (Exception ex)
 477     {
 478     }
 479   }
 480
 481   void reset()
 482   {
 483     av.setGlobalColourScheme(oldcs);
 484     if (av.alignment.getGroups() != null)
 485     {
 486       Vector allGroups = ap.av.alignment.getGroups();
 487       SequenceGroup sg;
 488       for (int g = 0; g < allGroups.size(); g++)
 489       {
 490         sg = (SequenceGroup) allGroups.get(g);
 491         sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
 492       }
 493     }
 494   }
 495
 496   public void thresholdCheck_actionPerformed(ActionEvent e)
 497   {
 498     changeColour();
 499   }
 500
 501   public void annotations_actionPerformed(ActionEvent e)
 502   {
 503     changeColour();
 504   }
 505
 506   public void threshold_actionPerformed(ActionEvent e)
 507   {
 508     changeColour();
 509   }
 510
 511   public void thresholdValue_actionPerformed(ActionEvent e)
 512   {
 513     try
 514     {
 515       float f = Float.parseFloat(thresholdValue.getText());
 516       slider.setValue((int) (f * 1000));
 517     } catch (NumberFormatException ex)
 518     {
 519     }
 520   }
 521
 522   public void valueChanged()
 523   {
 524     if (currentColours.isSelected()
 525             && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
 526     {
 527       changeColour();
 528     }
 529
 530     currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;
 531     ap.paintAlignment(false);
 532   }
 533
 534   public void currentColours_actionPerformed(ActionEvent e)
 535   {
 536     if (currentColours.isSelected())
 537     {
 538       reset();
 539     }
 540
 541     maxColour.setEnabled(!currentColours.isSelected());
 542     minColour.setEnabled(!currentColours.isSelected());
 543
 544     changeColour();
 545   }
 546
 547   public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
 548   {
 549     changeColour();
 550   }
 551
 552 }